Figure 4. Functional roles of the Pol II BH residues during the backtracking revealed by cross-correlation analysis.

In each metastable state, the correlations were calculated between the Pol II residues and the DNA TN (a) or RNA 3′-end nucleotide (b), respectively. For DNA TN (a), two critical BH residues, T831 and Y836, are highlighted with sphere models. In both S1 and S2 states, residue T831 is tightly correlated with the TN. Compared with S1 state, the DNA TN enhances its correlations with the residue Y836 in S2 state because of increased flexibility. In S3 state, the TN further increases its correlations with residue Y836 by forming direct packing interactions, which is critical for the TN to cross over the BH. In S4 state, the tight correlation between the Y836 and TN remains. For the RNA 3′-end nucleotide (b), two BH residues, T827 and T831, and one Rpb2 residue Y769, are highlighted as sphere models. In S1 state, the T831 shows the strongest correlation with the RNA 3′-end nucleotide, and weakly correlated with T827 and Y769. In S2 state, the RNA 3′-end nucleotide loses the coupling with residue T831 and strengthens the correlations with residues T827 and Y769. Strikingly, in S3 state, the RNA 3′-end nucleotide is tightly coupled to the residue Y769 by forming stable packing interactions, and it is barely coupled with BH residues. In the final state, RNA 3′-end nucleotide shows the correlation with all of these three residues. For each representation, the RNA:DNA hybrid chains are shown in grey, the DNA TN in a and RNA 3′-end nucleotide in b are shown as grey sphere models. The colours of the Pol II residues, including the BH residues and the Rpb2 residue Y769, correspond to the colours in the spectrum bar on the left.